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Thread: L2 and FGC testing of U106

  1. #1
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    L2 and FGC testing of U106

    The L2 SNP is showing up in 28 out of 61 U106 FGC tests results (ie Y-Elite or WGS testing). The SNP is not found in any Big Y testing (nor in FGC's analysis of Big Y BAM files). It is showing up scattered throughout the various clades of U106.

    I believe this is likely a false positive result, but I wanted to see if anyone here is aware of this issue.
    Gedmatch DNA: M032736 Gedcom: 6613110.
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  3. #2
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    I am L2>Z49>S8183>Y4355 and I have a number of U106 matches @ FTDNA, I don't understand the results but I guess that is what you call False Positive ?

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    Just an idea. For L2, the reference allele is T and L2 is C to T mutation - i.e. reference allele means L2 positive.

    http://ybrowse.org/gb2/gbrowse/chrY/?name=L2

    All YFull L2+ are U106-.
    Y-DNA: R-Y14088 (ISOGG: R1b1a1a2a1a2b1c2b1a1a)
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    Quote Originally Posted by Wing Genealogist View Post
    The L2 SNP is showing up in 28 out of 61 U106 FGC tests results (ie Y-Elite or WGS testing). The SNP is not found in any Big Y testing (nor in FGC's analysis of Big Y BAM files). It is showing up scattered throughout the various clades of U106.

    I believe this is likely a false positive result, but I wanted to see if anyone here is aware of this issue.
    Post from Richard Rocca from 2015
    "Since the reference human genome is composed on segments from multiple men, the derived/ancestral values are not consistent. One of the men is a U152+L2+Z367+L20+ male. So, all values like L2, Z367 and L20 are all reversed for someone that is truly L2. Not so for U152, so it gets complicated."

    https://anthrogenica.com/showthread....ll=1#post93756
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    Petr Just an idea. For L2, the reference allele is T and L2 is C to T mutation - i.e. reference allele means L2 positive.

    http://ybrowse.org/gb2/gbrowse/chrY/?name=L2

    MitchellSince1893 Post from Richard Rocca from 2015 "Since the reference human genome is composed on segments from multiple men, the derived/ancestral values are not consistent. One of the men is a U152+L2+Z367+L20+ male. So, all values like L2, Z367 and L20 are all reversed for someone that is truly L2. Not so for U152, so it gets complicated."

    [url]https://anthrogenica.com/showthread.php?4723-Dissection-of-the-Y-SNP-S116-in-Atlantic-Europe-and-Iberia-Valverde-et-al-2015&p=93756&viewfull=1#post93756[/url
    After FTDNA conversion to Hg38, I am R>R1b>M269>U152>L2>Z367>L20>CTS9733>S10068>BY3406 9 . What am I to make of what you are writing about? I am confused but I suppose it is due to my limited knowledge.
    Last edited by Celt_??; 02-10-2018 at 02:52 AM.
    FTDNA Big-Y SNP Results: R1b-U152+, L2+, Z367+, Z384+, L20+, CTS9733+, S10068+, BY33970

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    Quote Originally Posted by Celt_?? View Post
    After FTDNA conversion to Hg38, I am R>R1b>M269>U152>L2>Z367>L20>CTS9733>S10068>BY3406 9 . What am I to make of what you are writing about? I am confused but I suppose it is due to my limited knowledge.
    Best thing to do is to use Ybrowse and compare it to your BigY result
    e.g. on Ybrowse S10068 mutation: C to T.

    Go to BigY Results
    Go to the named variants tab and change the Derived window from "Yes" to "Show All"
    Type in S10068 and hit enter (on my computer there is a 15 second delay before anything happens). Eventually it will appear.
    Click on S10068 and a window will open. You should see "T" reads
    Last edited by MitchellSince1893; 02-10-2018 at 03:11 AM.
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    Quote Originally Posted by MitchellSince1893 View Post
    Best thing to do is to use Ybrowse and compare it to your BigY result e.g. on Ybrowse S10068 mutation: C to T.

    Go to BigY Results. Go to the named variants tab and change the Derived window from "Yes" to "Show All" Type in S10068 and hit enter (on my computer there is a 15 second delay before anything happens). Eventually it will appear.
    Click on S10068 and a window will open. You should see "T" reads
    Thank you, Mark. Interesting. For SNP S10068, it is quite clear; all reads for me - forward (blue) and reverse (green) - are "T". However, it becomes interesting for L2 and L20 - perhaps this is why you suggested S10068.

    For L2, I have three results: 2 forward are "C" and one reverse is "C". My genotype is given as "T" . For L20, I have two reverse results of "G" and "T" . My genotype is given as "A".

    If you have time to explain, I would appreciate your explanation. Best regards
    FTDNA Big-Y SNP Results: R1b-U152+, L2+, Z367+, Z384+, L20+, CTS9733+, S10068+, BY33970

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    Quote Originally Posted by Celt_?? View Post
    Thank you, Mark. Interesting. For SNP S10068, it is quite clear; all reads for me - forward (blue) and reverse (green) - are "T". However, it becomes interesting for L2 and L20 - perhaps this is why you suggested S10068.

    For L2, I have three results: 2 forward are "C" and one reverse is "C". My genotype is given as "T" . For L20, I have two reverse results of "G" and "T" . My genotype is given as "A".

    If you have time to explain, I would appreciate your explanation. Best regards
    I'm wondering if the issue is how you are interpreting the results. This is how a L2 positive result would look. Notice they are 29 "T" reads and 3 "C" reads
    l2 reads.png

    Again the reason this result looks different from other positive SNP results is that is the case of L2 and L20, the genotype and reference are the same (reason listed in post 4 above)
    Last edited by MitchellSince1893; 02-10-2018 at 03:54 PM.
    Y DNA line continued: Z142>Z12222>FGC12378>FGC12401>FGC12384
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    Quote Originally Posted by MitchellSince1893 View Post
    I'm wondering if the issue is how you are interpreting the results. This is how a L2 positive result would look. Notice they are 29 "T" reads and 3 "C" reads
    l2 reads.png

    Again the reason this result looks different from other positive SNP results is that is the case of L2 and L20, the genotype and reference are the same (reason listed in post 4 above)
    My confusion was that the "T" reads are not printed - as in your posted image. So the general rule must be that if no result it printed like in this case for "T", it is assumed that the reads are the reference value. Thanks a million!
    FTDNA Big-Y SNP Results: R1b-U152+, L2+, Z367+, Z384+, L20+, CTS9733+, S10068+, BY33970

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    Quote Originally Posted by Celt_?? View Post
    ...So the general rule must be that if no result it printed like in this case for "T", it is assumed that the reads are the reference value. Thanks a million!
    Yes, and in order to get the full picture cross check the SNP in ybrowse to see what the value should be if you have that mutation.
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